Togolese attacker Serge Gakpe profited from Rod Fanni's dreadful back-pass attempt to give the hosts the lead after 20 minutes and Marcelo Bielsa's out-of-form side could not find a way back, meaning they could find themselves 10 points from the summit on Sunday.
The visitors had their chances to punish Nantes on the day, but proved to be the architects of their own downfall, as Gakpe pounced on Fanni's poor pass to Steve Mandanda before slotting under the French goalkeeper.
Bielsa reacted at the break by introducing mercurial wideman Florian Thauvin for midfielder Giannelli Imbula and the winger proved a tricky customer in periods.
But Nantes goalkeeper Remy Riou remained largely untroubled until the latter stages, stopping Thauvin's drive in straightforward fashion with four minutes to go, before Andre Ayew picked up a booking for appearing to dive inside the area.
Fanni almost redeemed himself but saw his header tipped onto the crossbar in stoppage time as Marseille lost for the third league game running.
Marseille's desperate late pressure almost paid off, but Riou tipped Fanni's header onto the crossbar deep into stoppage time and Nantes held on, inflicting a third successive Ligue 1 loss on Marseille.
